Standards for public health genomic epidemiology to improve

Standards for public health genomic epidemiology to improve infec7ous disease outbreak detec7on and inves7ga7on Mélanie Courtot, Ph.D. mcourtot@gmail.com @mcourtot Simon Fraser University and BC Public Health Microbiology and Research Laboratory 8th Interna*onal Biocura*on Conference, April 26th 2015 h$p://www.slideshare.net/mcourtot 1 2 Source: Interna-onal Associa-on for Food Protec-on Each year, one in eight Canadians (or four million people) get sick with a domes7cally acquired food-­‐borne illness. 3 4 Source: Peter Gleick, Scienceblogs.com 5 6 7 Current Methods of Characterizing Foodborne Pathogens in a Public Health Laboratory • Growth characterisKcs • Phenotypic panels • AggluKnaKon reacKons • Enzyme immuno assays (EIAs) • PCR • DNA arrays (hybridizaKon) • Sanger sequencing • DNA restricKon • Electrophoresis (PFGE, capillary) Each pathogen is characterized by methods that are specific to that pathogen in mulKple workflows (separate workflows for each pathogen) TAT: 5 min – weeks (months) Source: Rebecca Lindsey 8 9 Laboratory
Test centric
Clinical
Patient centric
Epidemiology
Case centric
10 Source: Jennifer Gardy 11 2011 E. coli O104:H4 German outbreak Germany Egypt -­‐ 53 deaths, 3950 ill -­‐ Farmers compensated €210 million by EU Source: Fiona Brinkman 12 The IRIDA pla^orm Provincial
Public Health Agency
Academic/Public
(Integrated Rapid InfecKous Disease Analysis) fills in selected key bioinformaKcs gaps, to support real-­‐Kme infecKous disease outbreak invesKgaKons in Canada National
Public Health Agency
13 Open source, standards compliant, resource for public health agencies that can interact with, and complement, other ini-a-ves 13 IRIDA Annual General Mee7ng Winnipeg, April 8-­‐9, 2015 14 14 15 NML Phagetyping MLVA CGF PFGE Na7onal HA (NESP, PulseNet -­‐ Canada) PANORAMA PHRDWMart Sunquest paper BC PHMRL Public HA Sunquest PFGE Pa$erns AR, Biochemical Tests Various ReporKng Systems Strain sent to BC CDC Local HA BC CDC Epi paper (Crystal Reports) CNPHI PLIS PLIS paper Pa7ent Doctor Private or Hospital Lab MHO LHA 16 16 Source: Emma Griffiths IRIDA PLATFORM
Data
Sources
Clinical data
Epidemiology
data
IRIDA modules
End Users
Quality
Control
Med-Microbiologist
Lab Technologist
Lab-analysis Ready
Data
API
Data
processing
Data
storage
Analysis
Laboratory
data
Visualization
Researcher
Interactive Genome
Browser
Discovery Platform
Value
added
Activities
and
Analyses
Data
export
Epidemiologist
Epi-analysis Ready
Data
ONTOLOGY & DATA STANDARDS
Alert from
Laboratory/
Health
Authority
OUTBREAK
INVESTIGATION
OUTBREAK
CONCLUSION & REPORTING
17 How do we build those standards? 18 Interviews with key personnel 19 Laboratory(information(
(
TypON&
The(Typing(ontology(
!
Designed(with(the(goal(of(having(a(machine9readable(
language(that(describes(the(field(of(microbial(typing(
OBI&
Ontology(for(Biomedical(
OBI(is(an(ontology(of(investigations,(the(protocols(and(
Investigations(
instrumentation(used,(the(material(used,(the(data(generated(
and(the(types(of(analysis(performed(on(it.(
Next(Generation(Sequencing(
(
NGSOnto&
Next(Generation(Sequencing(
An(ontology(to(describe(workflows(in(a(Whole(Genome(
Ontology(
Sequencing(experiment.(Fairly(recent(effort(which(needs(to(
be(expanded.(
NIAID0GSC0
NIAID,(GSCID(and(BRC(Core(
A(standard(to(annotate(core(metadata(for(those(consortia.(
BRC&
metadata(
Very(high(level,(and(extends(OBI.(
MIxS&
An(ontological(representation(of( Work(in(progress(with(the(GSC.(
ontology&
the(MIxS(standard(
Epidemiology(
(
TRANS&
Pathogen(Transmission(
Describes(a(process(that(is(the(means(of(how(a(pathogen(is(
Ontology(
transmitted(from(one(host,(reservoir,(or(source(to(another(
host.(
ExO&
Exposure(ontology(
Exposure(information(for(toxicology,(epidemiology,(disease(
surveillance,(and(epigenetics(
EPO&
Designed(to(support(the(semantic(annotation(of(
Epidemiology(Ontology(
epidemiology(resources.(A(translation(of(the(Porta(Dictionary(
of(Epidemiology.(
IDO&
A(small(middle9level(resource(aimed(at(representing(terms(
Infectious(Disease(Ontology(
common(for(infectious(diseases,(such(as(pathogen.(
Food(
USDA&
USDA(Nutrient(Database(
Nutrient information on over 8,000 foods. Very
detailed, but not very categorized.(
EFSA&
European(Food(Safety(Authority( Huge resource, available via browsing tool and PDF
documentation.
Comprehensive(Food(
Consumption(Database(
Review exisKng resources 20 Metadata category Example Sample collec7on metadata Geographical loca-on, date, collector Sample source metadata Host, host body site, disease status Environmental metadata Temperature, pH, turbidity Lab analy7c PFGE paTern, MLST, CGF Sequencing metadata PlaWorm, Read length, Sequencing kit Assembly process/QC Coverage, nb of con-gs Pa7ent demographic Name, age, sex, physician 21 22 23 Source: h$p://learn.geneKcs.utah.edu/content/gsl/diversity/ What’s next? 24 • 
• 
• 
Load exis7ng datasets on the first version of IRIDA Annotate and integrate the data Validate the ontology content and its implementa7on DATA VALIDATION Validate ontology and pla^orm 25 INTERFACE SUPPORT Enable flexible user-­‐specific interface Source: Damion Dooley 26 IslandViewer Dhillon and Laird et al. 2015, Nucleic Acids Research 27 h$p://pathogenomics.sfu.ca/islandviewer IRIDA SNVPhyl pipeline IRIDA SNVPhyl pipeline output in GenGis, unpublished h$p://kiwi.cs.dal.ca/GenGIS/Main_Page 28 #1. Genomic epidemiology can help detect infecKous disease outbreak earlier #2. Integrated Rapid Infec7ous Disease Analysis plaaorm deployed in Canada, supported by a set of ontologies and standards #3. IRIDA capitalizes on exis7ng resources to make genomic epidemiology a pracKcal reality 29 Acknowledgements McMaster University Andrew McArthur Daim Sardar European Nucleo7de Archive Guy Cochrane Petra ten Hoopen Clara Amid European Food Safety Agency Leibana Criado Ernesto Vernazza Francesco Rizzi ValenKna Project Leaders Fiona Brinkman – SFU Will Hsiao – PHMRL Gary Van Domselaar – NML University of Lisbon Joᾶo Carriҫo Na7onal Microbiology Laboratory (NML) Franklin Bristow Aaron Petkau Thomas Ma$hews Josh Adam Adam Olsen Tara Lynch Shaun Tyler Philip Mabon Philip Au Celine Nadon Ma$hew Stuart-­‐Edwards Morag Graham Chrystal Berry Lorelee Tsche$er Laboratory for Foodborne Zoonoses (LFZ) Eduardo Toboada Peter Kruczkiewicz Chad Laing Vic Gannon Ma$hew Whiteside Ross Duncan Steven Mutschall Simon Fraser University (SFU) Melanie Courtot Emma Griffiths Geoff Winsor Julie Shay Ma$hew Laird Bhav Dhillon Raymond Lo BC Public Health Microbiology & Reference Laboratory (PHMRL) and BC Centre for Disease Control (BCCDC) Judy Isaac-­‐Renton Patrick Tang Natalie Prystajecky Jennifer Gardy Damion Dooley Linda Hoang Kim MacDonald Yin Chang Eleni Galanis Marsha Taylor Cletus D’Souza Ana Paccagnella University of Maryland Lynn Schriml Canadian Food Inspec7on Agency (CFIA) Burton Blais Catherine Carrillo Dominic Lambert Dalhousie University Rob Beiko 30 Alex Keddy Lisbon, Portugal July 28th 2015 hfp://purl.org/net/mcourtot/2015genomics.html 31